Ensuring citations next to every time a figure from the original arti…

…cle is used

evaluation/reproduction_success.qmd

@@ -1,5 +1,6 @@
 ---
 title: "Reproduction success"
+bibliography: ../quarto_site/references.bib
 ---
 
 Of the three items in the scope, 100% (3 out of 3) were considered to be **successfully reproduced**.
@@ -8,7 +9,7 @@ In each case, it was felt that there were **minimal variation** between the orig
 
 ## Figure 2
 
-Original figure:
+Original figure (@allen_simulation_2020):
 
 ![](../original_study/article_fig2.png){width=70% fig-align="center"}
 
@@ -18,7 +19,7 @@ Reproduction:
 
 ## Figure 3
 
-Original figure:
+Original figure (@allen_simulation_2020):
 
 ![](../original_study/article_fig3.png){width=70% fig-align="center"}
 
@@ -28,7 +29,7 @@ Reproduction:
 
 ## Figure 4
 
-Original figure:
+Original figure (@allen_simulation_2020):
 
 ![](../original_study/article_fig4.png){width=70% fig-align="center"}
 

evaluation/scope.qmd

@@ -1,5 +1,6 @@
 ---
 title: "Scope"
+bibliography: ../quarto_site/references.bib
 ---
 
 This page outlines that parts of the journal article which we will attempt to reproduce.
@@ -10,23 +11,23 @@ This page outlines that parts of the journal article which we will attempt to re
 
 ## Figure 2
 
-![Figure 2. "Patient state over time by unit. The patient population progresses through infection over three months (with 80% infected). The bold line shows the median results of 30 trials, and the fainter lines show the minimum and maximum from the 30 trials."](../original_study/article_fig2.png){width=80%}
+![Figure 2. "Patient state over time by unit. The patient population progresses through infection over three months (with 80% infected). The bold line shows the median results of 30 trials, and the fainter lines show the minimum and maximum from the 30 trials." @allen_simulation_2020](../original_study/article_fig2.png){width=80%}
 
 :::
 
 ::: {.callout-note appearance="minimal" collapse=true}
 
 ## Figure 3
 
-![Figure 3. "Progression of patient population through COVID infection, assuming 80% become infected over three months, with 15% mortality. The figure also shows the number of patients not allocated to a dialysis session at any time. The bold line shows the median results of 30 trials, and the fainter lines show the minimum and maximum from the 30 trials."](../original_study/article_fig3.png)
+![Figure 3. "Progression of patient population through COVID infection, assuming 80% become infected over three months, with 15% mortality. The figure also shows the number of patients not allocated to a dialysis session at any time. The bold line shows the median results of 30 trials, and the fainter lines show the minimum and maximum from the 30 trials." @allen_simulation_2020](../original_study/article_fig3.png)
 
 :::
 
 ::: {.callout-note appearance="minimal" collapse=true}
 
 ## Figure 4
 
-![Figure 4. "Patient displacement. The number of patients displaced from their current unit (left panel) and the additional travel time to the unit of care (right panel) for displaced patients. These results do not include those receiving inpatient care. The patient population progresses through infection over three months (with 80% infected). The bold line shows the median results of 30 trials, and the fainter lines show the minimum and maximum from the 30 trials."](../original_study/article_fig4.png)
+![Figure 4. "Patient displacement. The number of patients displaced from their current unit (left panel) and the additional travel time to the unit of care (right panel) for displaced patients. These results do not include those receiving inpatient care. The patient population progresses through infection over three months (with 80% infected). The bold line shows the median results of 30 trials, and the fainter lines show the minimum and maximum from the 30 trials." @allen_simulation_2020](../original_study/article_fig4.png)
 
 :::
 
@@ -38,7 +39,7 @@ This page outlines that parts of the journal article which we will attempt to re
 
 Outside scope as it is a table of model parameters rather than outputs.
 
-![Table 1. "Baseline model parameters."](../original_study/article_tab1.png)
+![Table 1. "Baseline model parameters." @allen_simulation_2020](../original_study/article_tab1.png)
 
 :::
 
@@ -48,7 +49,7 @@ Outside scope as it is a table of model parameters rather than outputs.
 
 Outside scope as it is a flow chart representing the model pathways.
 
-![Figure 1. "Schematic representation of patient pathway."](../original_study/article_fig1.png)
+![Figure 1. "Schematic representation of patient pathway." @allen_simulation_2020](../original_study/article_fig1.png)
 
 :::
 
@@ -58,7 +59,7 @@ Outside scope as it is a flow chart representing the model pathways.
 
 Outside scope as it is a result of the Monte Carlo model.
 
-![Figure 5. "One-way ambulance transport time distributions (1000 model runs). Results compare population COVID-positive and ambulance seating capacity (e.g. 2 = 2 seats.) Figures do not include ambulance clean-down/turnaround time."](../original_study/article_fig1.png)
+![Figure 5. "One-way ambulance transport time distributions (1000 model runs). Results compare population COVID-positive and ambulance seating capacity (e.g. 2 = 2 seats.) Figures do not include ambulance clean-down/turnaround time." @allen_simulation_2020](../original_study/article_fig5.png)
 
 :::
 
@@ -68,6 +69,6 @@ Outside scope as it is a result of the Monte Carlo model.
 
 Outside scope as it is a result of the Monte Carlo model.
 
-![Figure 6. "Two-way ambulance transport time distributions (1000 model runs). Results compare population COVID-positive and ambulance seating capacity (e.g. 2 = 2 seats.) Figures do not include ambulance clean-down/turnaround time."](../original_study/article_fig6.png)
+![Figure 6. "Two-way ambulance transport time distributions (1000 model runs). Results compare population COVID-positive and ambulance seating capacity (e.g. 2 = 2 seats.) Figures do not include ambulance clean-down/turnaround time." @allen_simulation_2020](../original_study/article_fig6.png)
 
 :::

logbook/posts/2024_05_22/index.qmd

@@ -3,6 +3,7 @@ title: "Day 1"
 author: "Amy Heather"
 date: "2024-05-22"
 categories: [setup, read, scope]
+bibliography: ../../../quarto_site/references.bib
 ---
 
 ::: {.callout-note}
@@ -79,13 +80,13 @@ Read article, making notes in `study_summary.qmd` (initially rough notes, then t
 * Defined period (e.g. one year). Patients progress through phases of COVID (negative, positive, some with inpatient care, recovred, died). In each COVID state, model seeks to put them in appropriate unit and session, opening COVID-positive sessions in units that allow it. COVID-positive don't mis with others.
 * Run 30 times, show median and extremes.
 
-![Patient pathway figure from Allen et al. 2020](../../../original_study/article_fig1.png){width=50%}
+![Patient pathway figure from @allen_simulation_2020](../../../original_study/article_fig1.png){width=50%}
 
 * All patients receive dialysis 3 times a week. Each patient starts on either Monday or Tuesday.
 * Have proportion of patients either fixed or sampled from stochastic distribution for phases of COVID state and care.
 * COVID seperate from uninfected and recovered.
 
-![Baseline model parameters from Allen et al. 2020](../../../original_study/article_tab1.png){width=50%}
+![Baseline model parameters from @allen_simulation_2020](../../../original_study/article_tab1.png){width=50%}
 
 For allocation to units, use search strategy:
 
@@ -109,11 +110,11 @@ COVID positive converted back to COVID negative when no longer needed.
 * Reduces workflow in units not taking COVID positive patients.
 * Displaced patients typically need 20 extra minutes to get to temporary care place (sometimes 50 minutes)
 
-![Figure 2](../../../original_study/article_fig2.png){width=50%}
+![Figure 2 - @allen_simulation_2020](../../../original_study/article_fig2.png){width=50%}
 
-![Figure 3](../../../original_study/article_fig3.png){width=50%}
+![Figure 3 - @allen_simulation_2020](../../../original_study/article_fig3.png){width=50%}
 
-![Figure 4](../../../original_study/article_fig4.png){width=50%}
+![Figure 4 - @allen_simulation_2020](../../../original_study/article_fig4.png){width=50%}
 
 **Discusion:**
 

logbook/posts/2024_05_23/index.qmd

@@ -3,6 +3,7 @@ title: "Day 2"
 author: "Amy Heather"
 date: "2024-05-23"
 categories: [read, reproduce]
+bibliography: ../../../quarto_site/references.bib
 ---
 
 ::: {.callout-note}
@@ -182,7 +183,7 @@ Updated the files accordingly.
 
 ### 14.19-15.12 Reproduction
 
-Original:
+Original (@allen_simulation_2020):
 
 <img src="../../../original_study/article_fig4.png" width="500" />
 
@@ -197,7 +198,7 @@ Run 2:
 * Ran again and compared images to see if its varying between runs - it looked quite different! I saved each under new file names so not overwritten
 * Model parameters input in the notebook look to match the paper (Table 1). Its 30 replications as in the paper too.
 
-![Table 1](../../../original_study/article_tab1.png)
+![Table 1 - @allen_simulation_2020](../../../original_study/article_tab1.png)
 
 ```
 number_of_replications = 30
@@ -251,7 +252,7 @@ Change random_state in parameters.py from None to having a value for each in the
 * NormalParams 1
 * UniformParams 2
 
-Original:
+Original (@allen_simulation_2020):
 
 <img src="../../../original_study/article_fig4.png" width="500" />
 

logbook/posts/2024_05_24/index.qmd

@@ -3,6 +3,7 @@ title: "Day 3"
 author: "Amy Heather"
 date: "2024-05-24"
 categories: [reproduce]
+bibliography: ../../../quarto_site/references.bib
 ---
 
 ::: {.callout-note}
@@ -56,6 +57,8 @@ Exploring methods for overlaying figures. Not timed as not about reproduction of
 
 Decided that it's not helpful to do this - spend more time fiddling around with getting them to resize and overlay correctly - and that the simplest option here would be to compare by eye.
 
+Base image sourced from @allen_simulation_2020
+
 If timed, 13.33-13.57.
 
 ```{python}

logbook/posts/2024_06_03/index.qmd

@@ -3,6 +3,7 @@ title: "Day 4"
 author: "Amy Heather"
 date: "2024-06-03"
 categories: [reproduce]
+bibliography: ../../../quarto_site/references.bib
 ---
 
 ::: {.callout-note}
@@ -75,7 +76,7 @@ Examples of differences to spot between them:
 * Interval of green line in Figure 2
 
 ::: {layout-ncol=3}
-Original Figure 2:
+Original Figure 2 (@allen_simulation_2020):
 <img src="../../../original_study/article_fig2.png" />
 
 Base 2700:
@@ -86,7 +87,7 @@ Base 2100:
 :::
 
 ::: {layout-ncol=3}
-Original Figure 3:
+Original Figure 3 (@allen_simulation_2020):
 <img src="../../../original_study/article_fig3.png" width="500" />
 
 Base 2700:
@@ -97,7 +98,7 @@ Base 2100:
 :::
 
 ::: {layout-ncol=3}
-Original Figure 4:
+Original Figure 4 (@allen_simulation_2020):
 <img src="../../../original_study/article_fig4.png" width="500" />
 
 Base 2700:

quarto_site/license.qmd

@@ -1,5 +1,6 @@
 ---
-title: "Open Source License"
+title: "Code and article licenses"
+bibliography: ../quarto_site/references.bib
 ---
 
 This repository is licensed under the MIT License.
@@ -12,7 +13,7 @@ This repository is licensed under the MIT License.
 
 :::
 
-This is aligned with the original study, who also licensed their work under the MIT License.
+This is aligned with the original study, who also licensed their code under the MIT License.
 
 ::: {.callout-note appearance="minimal" collapse=true}
 
@@ -22,3 +23,13 @@ This is aligned with the original study, who also licensed their work under the
 
 :::
 
+<!-- TODO: Add info about the article license -->
+The original study was published in the journal "PLOS ONE". They distributed the article under the Creative Commons Attribution 4.0 International (CC-BY-4.0) license. We have therefore been able to upload the article and images to this repository.
+
+::: {.callout-note appearance="minimal" collapse=true}
+
+## View copyright statement from journal
+
+"© 2020 Allen et al. This is an open access article distributed under the terms of the [Creative Commons Attribution License](http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited." - @allen_simulation_2020
+
+:::

quarto_site/references.bib

@@ -549,7 +549,7 @@ @article{zhang_reporting_2020
 	year = {2020},
 	keywords = {discrete event simulation, healthcare decision modeling, reporting quality checklist},
 	pages = {506--514},
-	file = {ScienceDirect Snapshot:/home/amy/Zotero/storage/YGMNWH9Z/S1098301520300401.html:text/html},
+	file = {Full Text:/home/amy/Zotero/storage/YW3KDRF5/Zhang et al. - 2020 - Reporting Quality of Discrete Event Simulations in.pdf:application/pdf;ScienceDirect Snapshot:/home/amy/Zotero/storage/YGMNWH9Z/S1098301520300401.html:text/html},
 }
 
 @misc{wickham_12_2023,
@@ -683,6 +683,56 @@ @article{monks_supplementary_2024
 	author = {Monks, Thomas and Harper, Alison},
 	month = jun,
 	year = {2024},
-	keywords = {Discrete-Event Simulation, Healthcare, Open models, Open Science, Systematic review},
+	keywords = {Systematic review, Discrete-Event Simulation, Healthcare, Open models, Open Science},
 	file = {Snapshot:/home/amy/Zotero/storage/BIVEYHET/11490636.html:text/html},
 }
+
+@misc{the_linux_foundation_docker_nodate,
+	title = {Docker containers: {What} are the open source licensing considerations?},
+	url = {https://www.linuxfoundation.org/resources/publications/docker-containers-what-are-the-open-source-licensing-considerations},
+	urldate = {2024-06-06},
+	journal = {The Linux Foundation},
+	author = {{The Linux Foundation}},
+	file = {Docker containers\: What are the open source licensing considerations?:/home/amy/Zotero/storage/X3LYAEL5/docker-containers-what-are-the-open-source-licensing-considerations.html:text/html},
+}
+
+@misc{noauthor_docker_nodate,
+	title = {Docker containers: {What} are the open source licensing considerations?},
+	shorttitle = {Docker containers},
+	url = {https://www.linuxfoundation.org/resources/publications/docker-containers-what-are-the-open-source-licensing-considerations},
+	abstract = {Tap into the latest open source publications. Discover insights from our projects and open technology thought leaders.},
+	language = {en},
+	urldate = {2024-06-06},
+	file = {Snapshot:/home/amy/Zotero/storage/XI6YY48D/docker-containers-what-are-the-open-source-licensing-considerations.html:text/html},
+}
+
+@misc{hoces_how_2020,
+	title = {How to {Teach} {Reproducibility} in {Classwork}},
+	url = {https://bitss.github.io/WEAI2020_slides},
+	abstract = {https://github.com/BITSS/WEAI2020\_slides},
+	urldate = {2024-06-12},
+	author = {Hoces, Fernando},
+	month = jun,
+	year = {2020},
+	file = {Hoces - 2020 - How to Teach Reproducibility in Classwork.pdf:/home/amy/Zotero/storage/P86MPQGM/Hoces - 2020 - How to Teach Reproducibility in Classwork.pdf:application/pdf},
+}
+
+@article{allen_simulation_2020,
+	title = {A simulation modelling toolkit for organising outpatient dialysis services during the {COVID}-19 pandemic},
+	volume = {15},
+	issn = {1932-6203},
+	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0237628},
+	doi = {10.1371/journal.pone.0237628},
+	abstract = {This study presents two simulation modelling tools to support the organisation of networks of dialysis services during the COVID-19 pandemic. These tools were developed to support renal services in the South of England (the Wessex region caring for 650 dialysis patients), but are applicable elsewhere. A discrete-event simulation was used to model a worst case spread of COVID-19, to stress-test plans for dialysis provision throughout the COVID-19 outbreak. We investigated the ability of the system to manage the mix of COVID-19 positive and negative patients, the likely effects on patients, outpatient workloads across all units, and inpatient workload at the centralised COVID-positive inpatient unit. A second Monte-Carlo vehicle routing model estimated the feasibility of patient transport plans. If current outpatient capacity is maintained there is sufficient capacity in the South of England to keep COVID-19 negative/recovered and positive patients in separate sessions, but rapid reallocation of patients may be needed. Outpatient COVID-19 cases will spillover to a secondary site while other sites will experience a reduction in workload. The primary site chosen to manage infected patients will experience a significant increase in outpatients and inpatients. At the peak of infection, it is predicted there will be up to 140 COVID-19 positive patients with 40 to 90 of these as inpatients, likely breaching current inpatient capacity. Patient transport services will also come under considerable pressure. If patient transport operates on a policy of one positive patient at a time, and two-way transport is needed, a likely scenario estimates 80 ambulance drive time hours per day (not including fixed drop-off and ambulance cleaning times). Relaxing policies on individual patient transport to 2-4 patients per trip can save 40-60\% of drive time. In mixed urban/rural geographies steps may need to be taken to temporarily accommodate renal COVID-19 positive patients closer to treatment facilities.},
+	language = {en},
+	number = {8},
+	urldate = {2024-06-17},
+	journal = {PLOS ONE},
+	author = {Allen, Michael and Bhanji, Amir and Willemsen, Jonas and Dudfield, Steven and Logan, Stuart and Monks, Thomas},
+	month = aug,
+	year = {2020},
+	note = {Publisher: Public Library of Science},
+	keywords = {Ambulances, COVID 19, Inpatients, Medical dialysis, Outpatients, Pandemics, Respiratory infections, Simulation and modeling},
+	pages = {e0237628},
+	file = {Full Text PDF:/home/amy/Zotero/storage/S5F2FSBS/Allen et al. - 2020 - A simulation modelling toolkit for organising outp.pdf:application/pdf},
+}